Search results for: gene frequency

Authors: Sandeep, A. Joshi, Kamal, Piu Dhibar, Parveen Kumar

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In the present work strong ground motion has been simulated using a modified semi-empirical technique (MSET), with frequency dependent radiation pattern model. Joshi et al. (2014) have modified the semi-empirical technique to incorporate the modeling of strong motion generation areas (SMGAs). A frequency dependent radiation pattern model is applied to simulate high frequency ground motion more precisely. Identified SMGAs (Kurahashi and Irikura 2012) of the 2011 Tohoku earthquake (Mw 9.0) were modeled using this modified technique. Records are simulated for both frequency dependent and constant radiation pattern function. Simulated records for both cases are compared with observed records in terms of peak ground acceleration and pseudo acceleration response spectra at different stations. Comparison of simulated and observed records in terms of root mean square error suggests that the method is capable of simulating record which matches in a wide frequency range for this earthquake and bears realistic appearance in terms of shape and strong motion parameters. The results confirm the efficacy and suitability of rupture model defined by five SMGAs for the developed modified technique.

Keywords: strong ground motion, semi-empirical, strong motion generation area, frequency dependent radiation pattern, 2011 Tohoku Earthquake

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Authors: Dian Ariyawati, Romi Sukoco, Sinung Agung Joko

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Background: Postural Orthostatic Tachycardia Syndrome (POTS) is a form of orthostatic intolerance caused by autonomic dysfunction. POTS predominantly occurs in young women. Regular exercise has proven to improve the organ system functions, including autonomous systems. The aim of this research was to determine the correlation between exercise frequency and POTS in young women. Method: 510 young women (16-23 years of age) were screened. They were obtained by interview and physical examination. The diagnosis of POTS was performed with Active Stand Test (AST) and heart rate measurement using a pulsemeter. There were 29 young women who suffered from POTS. The exercise frequency was obtained by interview. Data was statistically analyzed using Spearman Correlation test. Result: The subjects’, who tested positive for POTS didn’t perform regular exercise. The Spearman correlation test showed there was a moderate negative correlation between exercise frequency and POTS in young women (r = -0.487, p < 0.00). Conclusion: There is a moderate reverse correlation between exercise frequency and POTS in young women. Further studies are suggested to develop an exercise program for young who suffered from POTS.

Keywords: POTS, autonomic dysfunction, exercise frequency, young woman

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Authors: Ge Cui, Mei Fang Chien, Chihiro Inoue

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In this research, enrichment culture using an inorganic liquid medium collected soil contaminated with 1,2-dichlorobenzene (1,2-DCB) in Sendai, Japan, was added 1,2-DCB as the sole carbon source to create a stable consortium. The purpose of this research is to analysis dominant microorganisms in the stable consortium and enzyme system which play a role in the degradation of DCBs. The consortium is now at 30 generation and is still being cultured. By the result of PCR-DGGE and clone library, two bacteria are dominant. The bacteria named sk1 was isolated. 40mg/l of 1,2-DCB and 40mg/l of 1,4-DCB were completely degraded after 32 hours and 50 hours, respectively, but no degradation occurred in the case of 1,3-DCB. By PCR, tecA1 (α-subunit of DCB dioxygenase) gene which plays a role degrading DCB to DCB dihydrodiol, and tecB (dehydrogenase) gene which plays a role degrading DCB dihydrodiol to dichlorocatechol were amplified from strain sk1. Bacteria named sk100 was also isolated. 40mg/l of 1,2-DCB was completely degraded after 32 hours, but no degradation occurred in case of 1,3-DCB and 1,4-DCB. By the result of the catalytic core region of dioxygenase amplified by PCR, gene played a role degrading DCB was analyzed. The results of this study concluded that the isolated strains which have not been reported are able to degrade 1,2-DCB stably, and the characterization of degradation and the genomic analysis which is now in progress is helpful to have an overall view of this microbial degradation.

Keywords: DCB, 1, 2-DCB degrading strains, DCB dioxygenase, enrichment culture

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Authors: M. Marjaneh, M. Y. Narazah, H. Shahrul

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Array-based gene expression analysis is a powerful tool to profile expression of genes and to generate information on therapeutic effects of new anti-cancer compounds. Anti-apoptotic effect of thymoquinone was studied in MCF7 breast cancer cell line using gene expression profiling with cDNA micro array. The purity and yield of RNA samples were determined using RNeasyPlus Mini kit. The Agilent RNA 6000 Nano LabChip kit evaluated the quantity of the RNA samples. AffinityScript RT oligo-dT promoter primer was used to generate cDNA strands. T7 RNA polymerase was used to convert cDNA to cRNA. The cRNA samples and human universal reference RNA were labelled with Cy-3-CTP and Cy-5-CTP, respectively. Feature Extraction and GeneSpring software analysed the data. The single experiment analysis revealed involvement of 64 pathways with up-regulated genes and 78 pathways with down-regulated genes. The MAPK and p38-MAPK pathways were inhibited due to the up-regulation of PTPRR gene. The inhibition of p38-MAPK suggested up-regulation of TGF-ß pathway. Inhibition of p38 - MAPK caused up-regulation of TP53 and down-regulation of Bcl2 genes indicating involvement of intrinsic apoptotic pathway. Down-regulation of CARD16 gene as an adaptor molecule regulated CASP1 and suggested necrosis-like programmed cell death and involvement of caspase in apoptosis. Furthermore, down-regulation of GPCR, EGF-EGFR signalling pathways suggested reduction of ER. Involvement of AhR pathway which control cytochrome P450 and glucuronidation pathways showed metabolism of Thymoquinone. The findings showed differential expression of several genes in apoptosis pathways with thymoquinone treatment in estrogen receptor-positive breast cancer cells.

Keywords: cDNA microarray, thymoquinone, CARD16, PTPRR, CASP10

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Authors: M. Brandt, A. Peniak, J. Makarovič, P. Rafajdus

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This paper deals with a novel approach of power transformers diagnostics. This approach identifies the exact location and the range of a fault in the transformer and helps to reduce operation costs related to handling of the faulty transformer, its disassembly and repair. The advantage of the approach is a possibility to simulate healthy transformer and also all faults, which can occur in transformer during its operation without its disassembling, which is very expensive in practice. The approach is based on creating frequency dependent impedance of the transformer by sweep frequency response analysis measurements and by 3D FE parametrical modeling of the fault in the transformer. The parameters of the 3D FE model are the position and the range of the axial short circuit. Then, by comparing the frequency dependent impedances of the parametrical models with the measured ones, the location and the range of the fault is identified. The approach was tested on a real transformer and showed high coincidence between the real fault and the simulated one.

Keywords: transformer, parametrical model of transformer, fault, sweep frequency response analysis, finite element method

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Authors: Lucia Hrebeňárová, Jarmila Žolnová, Veronika Palková

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Inclusive education of students with special educational needs has been on the increase in the Slovak Republic, facing many challenges. Preparedness of teachers for inclusive education is one of the most frequent issues; teachers lack skills when it comes to the use of effective instruction depending on the individual needs of students, improvement of classroom management and social skills, and support of inclusion within the classroom. Social support is crucial for the school success of students within inclusive settings. The aim of the paper is to analyse perception of the frequency and importance of peer social support by students with special educational needs in inclusive education. The data collection tool used was the Child and Adolescent Social Support Scale (CASSS). The research sample consisted of 953 fourth grade students – 141 students with special educational needs educated in an inclusive setting and 812 students of the standard population. No significant differences were found between the students with special educational needs and the students without special educational needs in an inclusive setting when it comes to the perception of frequency and importance of social support of schoolmates and friends. However, the perception of frequency and importance of a friend’s social support was higher than the perception of frequency and importance of a classmate’s social support in both groups of students.

Keywords: inclusive education, peer social support, peer, student with special eEducational needs

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Authors: Jiri Brozovsky

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Modulus of elasticity is one of the important parameters of construction materials, which considerably influence their deformation properties and which can also be determined by means of non-destructive test methods like ultrasonic pulse method. However, measurement results of ultrasonic pulse methods are influenced by various factors, one of which is the natural frequency of the transducers. The paper states knowledge about influence of natural frequency of the transducers (54; 82 and 150kHz) on ultrasonic pulse velocity and dynamic modulus of elasticity (Young's Dynamic modulus of elasticity). Differences between ultrasonic pulse velocity and dynamic modulus of elasticity were found with the same smallest dimension of test specimen in the direction of sounding and density their value decreases as the natural frequency of transducers grew.

Keywords: calcium silicate brick, ultrasonic pulse method, ultrasonic pulse velocity, dynamic modulus of elasticity

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Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

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Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

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Authors: D. Mohammadzadeh S., J. Bolouri Bazaz

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This paper presents a new prediction model for compression index of fine-grained soils using multi-gene genetic programming (MGGP) technique. The proposed model relates the soil compression index to its liquid limit, plastic limit and void ratio. Several laboratory test results for fine-grained were used to develop the models. Various criteria were considered to check the validity of the model. The parametric and sensitivity analyses were performed and discussed. The MGGP method was found to be very effective for predicting the soil compression index. A comparative study was further performed to prove the superiority of the MGGP model to the existing soft computing and traditional empirical equations.

Keywords: new prediction model, compression index soil, multi-gene genetic programming, MGGP

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Authors: Ali Aydin, Mert Sudagidan, Aysen Coban, Alparslan Kadir Devrim

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Pseudomonas spp. (specifically, P. fluorescens and P. fragi) are considered the principal spoilage microorganisms of refrigerated poultry meats. The higher the level psychrophilic spoilage Pseudomonas spp. on carcasses at the end of processing lead to decrease the shelf life of the refrigerated product. The aim of the study was the identification of psychrophilic Pseudomonas spp. having proteolytic and lipolytic activities from poultry meats by 16S rRNA and rpoB gene sequencing, investigation of protease and lipase related genes and determination of proteolytic activity of Pseudomonas spp. In the of isolation procedure, collected chicken meat samples from local markets and slaughterhouses were homogenized and the lysates were incubated on Standard method agar and Skim Milk agar for selection of proteolytic bacteria and tributyrin agar for selection of lipolytic bacteria at +4 °C for 7 days. After detection of proteolytic and lipolytic colonies, the isolates were firstly analyzed by biochemical tests such as Gram staining, catalase and oxidase tests. DNA gene sequencing analysis and comparison with GenBank revealed that 126 strong enzyme Pseudomonas spp. were identified as predominantly P. fluorescens (n=55), P. fragi (n=42), Pseudomonas spp. (n=24), P. cedrina (n=2), P. poae (n=1), P. koreensis (n=1), and P. gessardi (n=1). Additionally, protease related aprX gene was screened in the strains and it was detected in 69/126 strains, whereas, lipase related lipA gene was found in 9 Pseudomonas strains. Protease activity was determined using commercially available protease assay kit and 5 strains showed high protease activity. The results showed that psychrophilic Pseudomonas strains were present in chicken meat samples and they can produce important levels of proteases and lipases for food spoilage to decrease food quality and safety.

Keywords: Pseudomonas, chicken meat, protease, lipase

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Authors: Rostika Flora, Muhammad Zulkarnain, Syokumawena

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Background: Aerobic physical exercises are recommended to keep body fit and healthy although physical exercises themselves can increase body metabolism and oxygen and can lead into tissue hypoxia. Oxygen pressure can serve as Vascular Endhothelial Growth Factor (VEGF) regulator. Hypoxia increases gene expression of VEGF through ascendant regulation of HIF-1. VEGF is involved in regulating angiogenesis process. Aerobic physical exercises can increase the concentration of VEGF in brain and enables angiogenesis process. We have investigated the influence of aerobic physical exercise to the VGEF concentration of wistar rat’s brain. Methods: This was experimental study using post test only control group design. Independent t-test was used as statistical test. The samples were twenty four wistar rat (Rattus Norvegicus) which were divided into four groups: group P1 (control group), group P2 (treatment group with once-a-week exercise), group P3 (treatment group with three time-a-week exercise), and group P4 (treatment group with seven time-a-week exercise). Group P2, P3, and P4 were treated with treadmil with speed of 20 m/minute for 30 minutes. The concentration of VEGF was determined by ELISA. Results: There was a significant increase of VEGF in treatment group compared with control one (<0.05). The maximum increase was found in group P2 (129.02±64.49) and the minimum increase was in group P4 (96.98±11.20). Conclusion: The frequency of aerobic physical exercises influenced the concentration of Vascular Endhothelial Growth Factor (VEGF) of brain tissue of Rattus Norvegicus.

Keywords: brain tissue, hypoxia, physical exercises, vascular endhothelial growth factor

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Authors: Md Monir Hossain, Anne Staples, Kuya Takami, Tomonari Furukawa

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Tire noise has a significant impact on ride quality and vehicle interior comfort, even at low frequency. Reduction of tire noise is especially important due to strict state and federal environmental regulations. The primary sources of tire noise are the low frequency structure-borne noise and the noise that originates from the release of trapped air between the tire tread and road surface during each revolution of the tire. The frequency response of the tire changes at low and high frequency. At low frequency, the tension and bending moment become dominant, while the internal structure and local deformation become dominant at higher frequencies. Here, we analyze tire response in terms of deformation and rolling velocity at low revolution frequency. An Abaqus FEA finite element model is used to calculate the static and dynamic response of a rolling tire under different rolling conditions. The natural frequencies and mode shapes of a deformed tire are calculated with the FEA package where the subspace-based steady state dynamic analysis calculates dynamic response of tire subjected to harmonic excitation. The analysis was conducted on the dynamic response at the road (contact point of tire and road surface) and side nodes of a static and rolling tire when the tire was excited with 200 N vertical load for a frequency ranging from 20 to 200 Hz. The results show that frequency has little effect on tire deformation up to 80 Hz. But between 80 and 200 Hz, the radial and lateral components of displacement of the road and side nodes exhibited significant oscillation. For the static analysis, the fluctuation was sharp and frequent and decreased with frequency. In contrast, the fluctuation was periodic in nature for the dynamic response of the rolling tire. In addition to the dynamic analysis, a steady state rolling analysis was also performed on the tire traveling at ground velocity with a constant angular motion. The purpose of the computation was to demonstrate the effect of rotating motion on deformation and rolling velocity with respect to a fixed Newtonian reference point. The analysis showed a significant variation in deformation and rolling velocity due to centrifugal and Coriolis acceleration with respect to a fixed Newtonian point on ground.

Keywords: natural frequency, rotational motion, steady state rolling, subspace-based steady state dynamic analysis

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Authors: D. Habibinia, M. R. Feyzi

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Nowadays, specialized software is vastly used to verify the performance of an electric machine prototype by evaluating a model of the system. These models mainly consist of electrical parameters such as inductances and resistances. However, when the operating frequency of the device is above one kHz, the effect of parasitic capacitances grows significantly. In this paper, a software-based procedure is introduced to model these capacitances within the electromagnetic simulation of the device. The case study is a high-frequency high-voltage pulse transformer. The Finite Element Analysis (FEA) software with coupled field analysis is used in this method.

Keywords: finite element analysis, parasitic capacitance, pulse transformer, high frequency

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Authors: Emanuela Chiarella, Annamaria Aloisio, Nisticò Clelia, Maria Mesuraca

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ZNF521 is a stem cell-associated transcription co-factor, that plays a crucial role in the homeostatic regulation of the stem cell compartment in the hematopoietic, osteo-adipogenic, and neural system. In normal hematopoiesis, primary human CD34+ hematopoietic stem cells display typically a high expression of ZNF521, while its mRNA levels rapidly decrease when these progenitors progress towards erythroid, granulocytic, or B-lymphoid differentiation. However, most acute myeloid leukemias (AMLs) and leukemia-initiating cells keep high ZNF521 expression. In particular, AMLs are often characterized by chromosomal translocations involving the Mixed Lineage Leukemia (MLL) gene, which MLL gene includes a variety of fusion oncogenes arisen from genes normally required during hematopoietic development; once they are fused, they promote epigenetic and transcription factor dysregulation. The chromosomal translocation t(9;11)(p21-22;q23), fusing the MLL gene with AF9 gene, results in a monocytic immune phenotype with an aggressive course, frequent relapses, and a short survival time. To better understand the dysfunctional transcriptional networks related to genetic aberrations, AML gene expression profile datasets were queried for ZNF521 expression and its correlations with specific gene rearrangements and mutations. The results showed that ZNF521 mRNA levels are associated with specific genetic aberrations: the highest expression levels were observed in AMLs involving t(11q23) MLL rearrangements in two distinct datasets (MILE and den Boer); elevated ZNF521 mRNA expression levels were also revealed in AMLs with t(7;12) or with internal rearrangements of chromosome 16. On the contrary, relatively low ZNF521 expression levels seemed to be associated with the t(8;21) translocation, that in turn is correlated with the AML1-ETO fusion gene or the t(15;17) translocation and in AMLs with FLT3-ITD, NPM1, or CEBPα double mutations. Invitro, we found that the enforced co-expression of ZNF521 in cord blood-derived CD34+ cells induced a significant proliferative advantage, improving MLL-AF9 effects on the induction of proliferation and the expansion of leukemic progenitor cells. Transcriptome profiling of CD34+ cells transduced with either MLL-AF9, ZNF521, or a combination of the two transgenes highlighted specific sets of up- or down-regulated genes that are involved in the leukemic phenotype, including those encoding transcription factors, epigenetic modulators, and cell cycle regulators as well as those engaged in the transport or uptake of nutrients. These data enhance the functional cooperation between ZNF521 and MA9, resulting in the development, maintenance, and clonal expansion of leukemic cells. Finally, silencing of ZNF521 in MLL-AF9-transformed primary CD34+ cells inhibited their proliferation and led to their extinction, as well as ZNF521 silencing in the MLL-AF9+ THP-1 cell line resulted in an impairment of their growth and clonogenicity. Taken together, our data highlight ZNF521 role in the control of self-renewal and in the immature compartment of malignant hematopoiesis, which, by altering the gene expression landscape, contributes to the development and/or maintenance of AML acting in concert with the MLL-AF9 fusion oncogene.

Keywords: AML, human zinc finger protein 521 (hZNF521), mixed lineage leukemia gene (MLL) AF9 (MLLT3 or LTG9), cord blood-derived hematopoietic stem cells (CB-CD34+)

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Authors: Mahbuba Rahman, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Darawan Rinchai, Damien Chaussabel, Nico Marr

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Collections of large-scale datasets made available in public repositories can be used to identify and fill gaps in biomedical knowledge. But first, these data need to be made readily accessible to researchers for analysis and interpretation. Here a collection of transcriptome datasets was made available to investigate the functional programming of human hematopoietic cells in early life. Thirty two datasets were retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom, interactive web application called the Gene Expression browser (GXB), designed for visualization and query of integrated large-scale data. Multiple sample groupings and gene rank lists were created based on the study design and variables in each dataset. Web links to customized graphical views can be generated by users and subsequently be used to graphically present data in manuscripts for publication. The GXB tool also enables browsing of a single gene across datasets, which can provide information on the role of a given molecule across biological systems. The dataset collection is available online. As a proof-of-principle, one of the datasets (GSE25087) was re-analyzed to identify genes that are differentially expressed by regulatory T cells in early life. Re-analysis of this dataset and a cross-study comparison using multiple other datasets in the above mentioned collection revealed that PMCH, a gene encoding a precursor of melanin-concentrating hormone (MCH), a cyclic neuropeptide, is highly expressed in a variety of other hematopoietic cell types, including neonatal erythroid cells as well as plasmacytoid dendritic cells upon viral infection. Our findings suggest an as yet unrecognized role of MCH in immune regulation, thereby highlighting the unique potential of the curated dataset collection and systems biology approach to generate new hypotheses which can be tested in future mechanistic studies.

Keywords: early-life, GEO datasets, PMCH, interactive query, systems biology

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Authors: Nan Deng, Zhenqiu Liu

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Thousands of patients with metastatic tumors were diagnosed with cancers of unknown primary sites each year. The inability to identify the primary cancer site may lead to inappropriate treatment and unexpected prognosis. Nowadays, a large amount of genomics and transcriptomics cancer data has been generated by next-generation sequencing (NGS) technologies, and The Cancer Genome Atlas (TCGA) database has accrued thousands of human cancer tumors and healthy controls, which provides an abundance of resource to differentiate cancer types. Meanwhile, deep convolutional neural networks (CNNs) have shown high accuracy on classification among a large number of image object categories. Here, we utilize 25 cancer primary tumors and 3 normal tissues from TCGA and convert their RNA-Seq gene expression profiling to color images; train, validate and test a CNN classifier directly from these images. The performance result shows that our CNN classifier can archive >80% test accuracy on most of the tumors and normal tissues. Since the gene expression pattern of distant metastases is similar to their primary tumors, the CNN classifier may provide a potential computational strategy on identifying the unknown primary origin of metastatic cancer in order to plan appropriate treatment for patients.

Keywords: bioinformatics, cancer, convolutional neural network, deep leaning, gene expression pattern

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Authors: K. R. Thabethe, G. A. Adefolaju, M. J. Hosie

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Cervical cancer is the third most commonly diagnosed cancer globally and it is one of three AIDS defining malignancies. Highly active antiretroviral therapy (HAART) is a combination of three or more antiretroviral drugs and has been shown to play a significant role in reducing the incidence of some AIDS defining malignancies, although its effect on cervical cancer is still unclear. The aim of this study was to investigate the relationship between cervical cancer and HAART. This was achieved by studying the expression of two signalling molecules expressed in cervical cancer; MUC1 and P65. Following the 24 hour treatment of a cervical cancer cell line, HCS-2, with drugs which are commonly used as part of HAART at their clinical plasma concentrations, real-time qPCR and immunofluorescence were used in order to study gene and protein expression. A one way ANOVA followed by a Tukey Kramer Post Hoc test was conducted using JMP 11 software on both sets of data. The drug classified as a protease inhibitor (PI) (i.e. LPV/r) reduced MUC1 and P65 gene and protein expression more than the other drug tested. PIs are known to play a significant role in cell death, therefore the cells were thought to be more susceptible to cell death following treatment with PIs. In conclusion, the drugs used, especially the PI showed some anticancer effects by facilitating cell death through decreased gene and protein expression of MUC1 and P65 and present promising agents for cancer treatment.

Keywords: cervical cancer, haart, MUC1, P65

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Authors: Siri-Orn Champatong

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This research paper was aimed to examine the relationship between visitors’ attitude towards the service marketing mix and visitors’ frequency of visit to Bangpu Recreation Centre. Based on a large and uncalculated population, the number of samples was calculated according to the formula to obtain a total of 385 samples. In collecting the samples, systematic random sampling was applied and by using of a Likert five-scale questionnaire for, a total of 21 days to collect the needed information. Mean, Standard Deviation, and Pearson’s basic statistical correlations were utilized in analyzing the data. This study discovered a high level of visitors’ attitude product and service of Bangpu Recreation Centre, price, place, promotional activities, people who provided service and physical evidence of the centre. The attitude towards process of service was discovered to be at a medium level. Additionally, the finding of an examination of a relationship between visitors’ attitude towards service marketing mix and visitors’ frequency of visit to Bangpu Recreation Centre presented that product and service, people, physical evidence and process of service provision showed a relationship with the visitors’ frequency of visit to the centre per year.

Keywords: frequency of visit, visitor, service marketing mix, Bangpu Recreation Centre

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

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Authors: Alina Smalinskiene Janina Petkeviciene, Jurate Klumbiene, Vilma Kriaucioniene, Vaiva Lesauskaite

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The worldwide prevalence of obesity has been increasing dramatically in the last few decades, and Lithuania is no exception. In 2012, every fifth adult (19% of men and 20.5 % of women) was obese and every third was overweight Association studies have highlighted the influence of SNPs in obesity, with particular focus on FTO rs9939609. Thus far, no data on the possible association of this SNP to obesity in the adult Lithuanian population has been reported. Here, for the first time, we demonstrate an association between the FTO rs9939609 homozygous AA genotype and increased BMI when compared to homozygous TT. Furthermore, a positive association was determined between the FTO rs9939609 variant and risk of metabolic syndrome. Background: This study aimed to examine the associations between the fat mass and obesity associated (FTO) gene rs9939609 variant with obesity and metabolic syndrome in Lithuanian adult population. Materials and Methods: A cross-sectional health survey was carried out in randomly selected municipalities of Lithuania. The random sample was obtained from lists of 25–64 year-old inhabitants. The data from 1020 subjects were analysed. The rs9939609 SNP of the FTO gene was assessed using TaqMan assays (Applied Biosystems, Foster City, CA, USA). The Applied Biosystems 7900HT Real-Time Polymerase Chain Reaction System was used for detecting the SNPs. Results: The carriers of the AA genotype had the highest mean values of BMI and waist circumference (WC) and the highest risk of obesity. Interactions ‘genotype x age’ and ‘genotype x physical activity’ in determining BMI and WC were shown. Neither lipid and glucose levels, nor blood pressure were associated with the rs9939609 independently of BMI. In the age group of 25-44 years, association between the FTO genotypes and metabolic syndrome was found. Conclusion: The FTO rs9939609 variant was significantly associated with BMI and WC, and with the risk of obesity in Lithuanian population. The FTO polymorphism might have a greater influence on weight status in younger individuals and in subjects with a low level of physical activity.

Keywords: obesity metabolic syndrome, FTO gene, polymorphism, Lithuania

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Authors: Shankha Sanyal, Archi Banerjee, Sayan Biswas, Sourya Sengupta, Sayan Nag, Ranjan Sengupta, Dipak Ghosh

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The term ‘gestalt’ has been widely used in the field of psychology which defined the perception of human mind to group any object not in part but as a 'unified' whole. Music, in general, is polyphonic - i.e. a combination of a number of pure tones (frequencies) mixed together in a manner that sounds harmonious. The study of human brain response due to different frequency groups of the acoustic signal can give us an excellent insight regarding the neural and functional architecture of brain functions. Hence, the study of music cognition using neuro-biosensors is becoming a rapidly emerging field of research. In this work, we have tried to analyze the effect of different frequency bands of music on the various frequency rhythms of human brain obtained from EEG data. Four widely popular Rabindrasangeet clips were subjected to Wavelet Transform method for extracting five resonant frequency bands from the original music signal. These frequency bands were initially analyzed with Detrended/Adaptive Fractal analysis (DFA/AFA) methods. A listening test was conducted on a pool of 100 respondents to assess the frequency band in which the music becomes non-recognizable. Next, these resonant frequency bands were presented to 20 subjects as auditory stimulus and EEG signals recorded simultaneously in 19 different locations of the brain. The recorded EEG signals were noise cleaned and subjected again to DFA/AFA technique on the alpha, theta and gamma frequency range. Thus, we obtained the scaling exponents from the two methods in alpha, theta and gamma EEG rhythms corresponding to different frequency bands of music. From the analysis of music signal, it is seen that loss of recognition is proportional to the loss of long range correlation in the signal. From the EEG signal analysis, we obtain frequency specific arousal based response in different lobes of brain as well as in specific EEG bands corresponding to musical stimuli. In this way, we look to identify a specific frequency band beyond which the music becomes non-recognizable and below which in spite of the absence of other bands the music is perceivable to the audience. This revelation can be of immense importance when it comes to the field of cognitive music therapy and researchers of creativity.

Keywords: AFA, DFA, EEG, gestalt in music, Hurst exponent

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Authors: T. C. C. Soo, S. Bhassu

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Unlike the common presence of both innate and adaptive immunity in vertebrates, crustaceans, in particular, shrimps, have been discovered to possess only innate immunity. This further emphasizes the importance of innate immunity within shrimps in pathogenic resistance. Under the study of pathogenic immune challenge, different shrimp species actually exhibit varying degrees of immune resistance towards the same pathogen. Furthermore, even within the same shrimp species, different batches of challenged shrimps can have different strengths of immune defence. Several important pathways are activated within shrimps during pathogenic infection. One of them is JAK-STAT pathway that is activated during bacterial, viral and fungal infections by which STAT(Signal Transducer and Activator of Transcription) gene is the core element of the pathway. Based on theory of Central Dogma, the genomic information is transmitted in the order of DNA, RNA and protein. This study is focused in uncovering the important evolutionary patterns present within the DNA (non-coding region) and RNA (coding region). The three shrimp species involved are Macrobrachium rosenbergii, Penaeus monodon and Litopenaeus vannamei which all possess commercial significance. The shrimp species were challenged with a famous penaeid shrimp virus called white spot syndrome virus (WSSV) which can cause serious lethality. Tissue samples were collected during time intervals of 0h, 3h, 6h, 12h, 24h, 36h and 48h. The DNA and RNA samples were then extracted using conventional kits from the hepatopancreas tissue samples. PCR technique together with designed STAT gene conserved primers were utilized for identification of the STAT coding sequences using RNA-converted cDNA samples and subsequent characterization using various bioinformatics approaches including Ramachandran plot, ProtParam and SWISS-MODEL. The varying levels of immune STAT gene activation for the three shrimp species during WSSV infection were confirmed using qRT-PCR technique. For one sample, three biological replicates with three technical replicates each were used for qRT-PCR. On the other hand, DNA samples were important for uncovering the structural variations within the genomic region of STAT gene which would greatly assist in understanding the STAT protein functional variations. The partially-overlapping primers technique was used for the genomic region sequencing. The evolutionary inferences and event predictions were then conducted through the Bayesian Inference method using all the acquired coding and non-coding sequences. This was supplemented by the construction of conventional phylogenetic trees using Maximum likelihood method. The results showed that adaptive evolution caused STAT gene sequence mutations between different shrimp species which led to evolutionary divergence event. Subsequently, the divergent sites were correlated to the differing expressions of STAT gene. Ultimately, this study assists in knowing the shrimp species innate immune variability and selection of disease resistant shrimps for breeding purpose. The deeper understanding of STAT gene evolution from the perspective of both purifying and adaptive approaches not only can provide better immunological insight among shrimp species, but also can be used as a good reference for immunological studies in humans or other model organisms.

Keywords: gene evolution, JAK-STAT pathway, immunology, STAT gene

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Authors: Ammar Said Ahmed, M. Reissmann, R. Bortfeldt, G. A. Brockmann

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Milk protein genetic variants are of interest for characterizing domesticated mammalian species and breeds, and for studying associations with economic traits. The aim of this work was to analyze milk protein genetic variation in the Sudanese native cattle breeds, which have been gradually declining in numbers over the last years due to the breed substitution, and indiscriminate crossbreeding. The genetic variation at three milk protein genes αS1-casein (CSN1S1), αS2-casein (CSN1S2) and ƙ-casein (CSN3) was investigated in 250 animals belonging to five Bos indicus cattle breeds of Sudan (Butana, Kenana, White-nile, Erashy and Elgash). Allele specific primers were designed for five SNPs determine the CSN1S1 variants B and C, the CSN1S2 variants A and B, the CSN3 variants A, B and H. Allele, haplotype frequencies and genetic distances (D) were calculated and the phylogenetic tree was constructed. All breeds were found to be polymorphic for the studied genes. The CSN1S1*C variant was found very frequently (>0.63) in all analyzed breeds with highest frequency (0.82) in White-nile cattle. The CSN1S2*A variant (0.77) and CSN3*A variant (0.79) had highest frequency in Kenana cattle. Eleven haplotypes in casein gene cluster were inferred. Six of all haplotypes occurred in all breeds with remarkably deferent frequencies. The estimated D ranged from 0.004 to 0.049. The most distant breeds were White-nile and Kenana (D 0.0479). The results presented contribute to the genetic knowledge of indigenous cattle and can be used for proper definition and classification of the Sudanese cattle breeds as well as breeding, utilization, and potential development of conservation strategies for local breeds.

Keywords: milk protein, genetic variation, casein haplotype, Bos indicus

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Authors: Oussema Tabbabi, Mondher Laabidi, Fethi Choubani, J. David

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This study presents a miniaturized antenna based on chiral metamaterials slotted ground plane. To decrease resonant frequency while keeping the antennas physical dimensions the same, we propose a two novel patch antennas with double Z and cross slots on the ground plane. The length of the each type of slot are also altered to investigate the effect on miniaturization performance. Resonance frequency reduction has been achieved nearly to 30% and 23% as well as size reduction of almost 28% and 22% for the double Z and the cross shape respectively.

Keywords: chiral metamaterials, miniaturized antenna, miniaturization, resonance frequency

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Authors: Danna Jia, Bin Li

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Background: Atopic dermatitis (AD) is a chronic and refractory inflammatory skin disease characterized by relapsing eczematous and pruritic skin lesions. The global prevalence of AD ranges from 1~ 20%, and its incidence rates are increasing. It affects individuals from infancy to adulthood, significantly impacting their daily lives and social activities. Despite its major health burden, the precise mechanisms underlying AD remain unknown. Understanding the genetic differences associated with AD is crucial for advancing diagnosis and targeted treatment development. This study aims to identify candidate genes of AD by using bioinformatics analysis. Methods: We conducted a comprehensive analysis of four pooled transcriptomic datasets (GSE16161, GSE32924, GSE130588, and GSE120721) obtained from the Gene Expression Omnibus (GEO) database. Differential gene expression analysis was performed using the R statistical language. The differentially expressed genes (DEGs) between AD patients and normal individuals were functionally analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, a protein-protein interaction (PPI) network was constructed to identify candidate genes. Results: Among the patient-level gene expression datasets, we identified 114 shared DEGs, consisting of 53 upregulated genes and 61 downregulated genes. Functional analysis using GO and KEGG revealed that the DEGs were mainly associated with the negative regulation of transcription from RNA polymerase II promoter, membrane-related functions, protein binding, and the Human papillomavirus infection pathway. Through the PPI network analysis, we identified eight core genes: CD44, STAT1, HMMR, AURKA, MKI67, and SMARCA4. Conclusion: This study elucidates key genes associated with AD, providing potential targets for diagnosis and treatment. The identified genes have the potential to contribute to the understanding and management of AD. The bioinformatics analysis conducted in this study offers new insights and directions for further research on AD. Future studies can focus on validating the functional roles of these genes and exploring their therapeutic potential in AD. While these findings will require further verification as achieved with experiments involving in vivo and in vitro models, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.

Keywords: atopic dermatitis, bioinformatics, biomarkers, genes

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Authors: Ali̇ Bayram, Semih Dalkilic, Remzi Yigiter

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N-methyl-D-aspartate (NMDA) receptor is a subtype of glutamate receptor and plays a pivotal role in learning, memory, neuronal plasticity, neurotoxicity and synaptic mechanisms. Animal experiments were suggested that glutamate-induced excitotoxic injuriy and NMDA receptor blockage lead to amnesia and other neurodegenerative diseases including Alzheimer’s disease (AD), Huntington’s disease, amyotrophic lateral sclerosis. Aim of this study is to investigate association between NMDA receptor coding gene GRIN2B expression level and Alzheimer disease. The study was approved by the local ethics committees, and it was conducted according to the principles of the Declaration of Helsinki and guidelines for the Good Clinical Practice. Peripheral blood was collected 50 patients who diagnosed AD and 49 healthy control individuals. Total RNA was isolated with RNeasy midi kit (Qiagen) according to manufacturer’s instructions. After checked RNA quality and quantity with spectrophotometer, GRIN2B expression levels were detected by quantitative real time PCR (QRT-PCR). Statistical analyses were performed, variance between two groups were compared with Mann Whitney U test in GraphpadInstat algorithm with 95 % confidence interval and p < 0.05. After statistical analyses, we have determined that GRIN2B expression levels were down regulated in AD patients group with respect to control group. But expression level of this gene in each group was showed high variability. İn this study, we have determined that NMDA receptor coding gene GRIN2B expression level was down regulated in AD patients when compared with healthy control individuals. According to our results, we have speculated that GRIN2B expression level was associated with AD. But it is necessary to validate these results with bigger sample size.

Keywords: Alzheimer’s disease, N-methyl-d-aspartate receptor, NR2B, GRIN2B, mRNA expression, RT-PCR

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Authors: Qingtao Yu, Guojia Ma

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Approaches to microwave absorption and low infrared emissivity are often conflicting, as the low-emissivity layer, usually consisting of metals, increases the reflection of microwaves, especially in high frequency. In this study, an infrared-radar compatible stealth surface was fabricated by first depositing a layer of low-emissivity metal film on the surface of a layer of radar-absorbing material. Then, ultrafast laser was used to generate patterns on the metal film, forming a frequency selective surface. With proper pattern design, while the majority of the frequency selective surface is covered by the metal film, it has relatively little influence on the reflection of microwaves between 2 to 18 GHz. At last, structures on the radar-absorbing layer were fabricated by ultra-fast laser to further improve the absorbing bandwidth of the microwave. This study demonstrates that the compatibility between microwave absorption and low infrared emissivity can be achieved by properly designing patterns and structures on the metal film and the radar-absorbing layer accordingly.

Keywords: frequency selective surface, infrared-radar compatible, low infrared emissivity, radar-absorbing material, patterns, structures

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Authors: Seung-Hwa Baek, In-Jung Nam, Sang-Han Lee

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The development of anti-melanogenic agents is important for the prevention of serious esthetic problem like a melasma, freckle, age spots, and chloasma. The aim of this study was to investigate the anti-melanogenic effect of sesamol, an active lignan isolated from sesame seed, by mushroom and cellular tyrosinase assay, melanin content and the analysis of melanogensis-related mRNA expressions in melana cells. Sesamol showed strong inhibitory activity against the mushroom tyrosinase in a dose-dependent manner. Intracellular tyrosinase inhibition activity was also confirmed by zymography. At a concentration of 50 μM, sesamol inhibited melanin production in melan-a cells with no cytoxicity while those of phenylthiourea (PTU) as a positive control were the same condition. Sesamol significantly inhibited the expression of melanogensis-related genes, such as tyrosinase, tyrosinase-related protein-1 (TRP-1), dopachrome tautomerase (Dct), microphthalmia-associated transcription factor (MITF) and melanocortin 1 receptor (MC1R). These findings indicate that sesamol could reduce melanin biosynthesis via the downregulation of tyrosinase activity and melanin production via subsequent gene expression of melanogenesis-related proteins. Together, these results suggest that the sesamol have strong potential in inhibiting melanin biosynthesis, in that the substance may be used as a new skin-whitening agent of cosmetic materials.

Keywords: sesamol, sesame seed, melanin biosynthesis, melanogenesis-related gene, skin-whitening agent

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Authors: Özlem Ateş Sönmezoğlu, Begüm Terzi, Ahmet Yıldırım, Ramazan Özbey

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The basic criteria which determine durum wheat quality is its suitability for pasta processing that is pasta making quality. Bright yellow color is a desired property in pasta products. Durum wheat pasta making quality is affected by grain pigment content and oxidative enzymes which affect adversely bright yellow color. Of the oxidative enzymes, lipoxygenase LOX is the most effective one on oxidative bleaching of yellow pigments in durum wheat products. Thus, wheat cultivars that are high in yellow pigments but low in LOX enzyme activity should be preferred for the production of pasta with high color quality. The aim of this study was to reduce lipoxygenase activities of the backcross durum wheat lines that were previously improved for their protein quality. For this purpose, two advanced lines with different parents (TMB2 and TMB3) were used recurrent parents. Also, Gediz-75 wheat with low LOX enzyme activity was used as the gene source. In all of the generations, backcrossed plants carrying the targeted gene region (Lpx-B1.1) were selected using SSR markers by marker assisted selection method. As a result, the study will be completed in three years instead of six years required in a classical backcross breeding study, leading to the development of high-quality candidate varieties. This research has been financially supported by TÜBİTAK (Project No: 112T910).

Keywords: durum wheat, lipoxygenase, LOX, Lpx-B1.1, MAS, Triticum durum

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Authors: Mansur Abdulrasheed, Hussein I. Ibrahim, Ahmed F. Umar

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Nitrification, the microbial oxidation of ammonia to nitrate (NO3-) via nitrite (NO2-) is a vital process in the biogeochemical nitrogen cycle and is performed by two distinct functional groups; ammonia oxidisers (comprised of ammonia oxidising bacteria (AOB) and ammonia oxidising archaea (AOA)) and nitrite oxidising bacteria. Autotrophic nitrification is said to occur in acidic soils, even though most laboratory cultures of isolated ammonia and nitrite oxidising bacteria fail to grow below neutral pH. Published studies revealed that soil pH is a major driver for determining the distribution and abundance of AOB and AOA. To determine whether distinct populations of nitrite oxidising bacteria within the lineages of Nitrospira and Nitrobacter are adapted to a particular range of pH as observed in ammonia oxidising organisms, the community structure of Nitrospira-like and Nitrobacter-like NOB were examined across a pH gradient (4.5–7.5) by amplifying nitrite oxido-reductase (nxrA) and 16S rRNA genes followed by denaturing gradient gel electrophoresis (DGGE). The community structure of both Nitrospira and Nitrobacter changed with soil pH, with distinct populations observed in acidic and neutral soils. The abundance of Nitrospira-like 16S rRNA and Nitrobacter-like nxrA gene copies contrasted across the pH gradient. Nitrobacter-like nxrA gene abundance decreased with increasing soil pH, whereas Nitrospira-like 16S rRNA gene abundance increased with increasing pH. Findings indicated that abundance and distributions of soil NOB is influence by soil pH.

Keywords: nitrospira, nitrobacter, nitrite-oxidizing bacteria, nitrification, pH, soil

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